Greg,
I figure it out. Adding const should work.
const Atom *atom = (*pCurrentROMol)[*atBegin];
Thanks.
Yingfeng
On Wed, Dec 12, 2018 at 10:21 AM Yingfeng Wang <ywang...@gmail.com> wrote:
> Greg,
>
> I figure out the problem. Removing "->get()" can solve the problem.
>
> Here is the updated version.
>
> boost::tie(firstB,lastB) = pCurrentROMol->getEdges();
>
> while(firstB!=lastB)
>
> {
>
> auto bond = (*pCurrentROMol)[*firstB];
>
> ...
>
> sEdgeLabel += ((queryIsBondInRing(bond)) ? "ring|" : "linear|" );
>
> ...
>
> ++firstB;
>
> }
>
>
> The original version was
>
>
> boost::tie(firstB,lastB) = pCurrentROMol->getEdges();
>
> while(firstB!=lastB)
>
> {
>
> boost::shared_ptr<Bond> bond = (*pCurrentROMol)[*firstB];
>
> ...
>
> sEdgeLabel += ((queryIsBondInRing(bond.get())) ? "ring|" : "linear|"
> );
>
> ...
>
> ++firstB;
>
> }
>
>
> However, I still have a question. Why "Atom *atom" and "Bond *bond" do not
> work? Yes, "auto" solves the problem, but I feel it just covers the
> essential issue.
>
>
> Thanks.
>
> Yingfeng
>
>
>
>
> On Wed, Dec 12, 2018 at 9:50 AM Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> Greg,
>>
>> Thanks. The first way does not work. I got the following error message.
>>
>> *Database.cpp:148:15: **error: **cannot initialize a variable of type
>> 'RDKit::Atom *'*
>>
>> * with an rvalue of type 'const RDKit::Atom *'*
>>
>> Atom *atom = (*pCurrentROMol)[*atBegin];
>>
>>
>> The second way, which uses "auto", works. I also updated the code for
>> bond and got a new error with the following error message.
>>
>> *Database.cpp:164:49: **error: **no member named 'get' in 'RDKit::Bond'*
>>
>> sEdgeLabel += ((queryIsBondInRing(bond->get())) ? "ring|" :
>> "linear|" );
>>
>> * ~~~~ ^*
>>
>> 1 error generated.
>>
>> Could you please confirm that the updated class Bond removes method
>> get()? If this is the case, which method should I use?
>>
>> Again, thank you very much for your help!
>>
>> Yingfeng
>>
>>
>>
>> On Wed, Dec 12, 2018 at 12:58 AM Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>
>>> Hi Yingfeng,
>>>
>>> As part of the move over to Modern C++ we also changed the way atoms and
>>> bonds are stored in molecules: you now get raw pointers back instead of
>>> smart pointers.
>>> If you change your code from:
>>> boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin];
>>> to:
>>> Atom *atom = (*pCurrentROMol)[*atBegin];
>>> or, even simpler:
>>> auto atom = (*pCurrentROMol)[*atBegin];
>>>
>>> things should work.
>>> -greg
>>>
>>>
>>> On Wed, Dec 12, 2018 at 12:36 AM Yingfeng Wang <ywang...@gmail.com>
>>> wrote:
>>>
>>>> I am using the C++ library of RDKit on Mac. My C++ code works with
>>>> RDKit_2017_09_3. However, after I switch to RDKit 2018_03_4, I got the
>>>> following error when compiling my C++ source code.
>>>>
>>>> *Database.cpp:148:33: **error: **no viable conversion from 'const
>>>> RDKit::Atom *' to*
>>>>
>>>> * 'boost::shared_ptr<Atom>'*
>>>>
>>>> boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin];
>>>>
>>>> * ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~*
>>>>
>>>> */usr/local/Cellar/boost/1.68.0/include/boost/smart_ptr/shared_ptr.hpp:358:21:
>>>> **note: *
>>>>
>>>> candidate constructor not viable: no known conversion from
>>>>
>>>> 'const RDKit::Atom *' to 'boost::detail::sp_nullptr_t' (aka
>>>> 'nullptr_t')
>>>>
>>>> for 1st argument
>>>>
>>>> BOOST_CONSTEXPR shared_ptr( boost::detail::sp_nullptr_t )
>>>> BOOST_SP_N...
>>>>
>>>> * ^*
>>>>
>>>> */usr/local/Cellar/boost/1.68.0/include/boost/smart_ptr/shared_ptr.hpp:422:5:
>>>> **note: *
>>>>
>>>> candidate constructor not viable: no known conversion from
>>>>
>>>> 'const RDKit::Atom *' to 'const boost::shared_ptr<RDKit::Atom>
>>>> &' for 1st
>>>>
>>>> argument
>>>>
>>>> shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ),
>>>> p...
>>>>
>>>> * ^*
>>>>
>>>> I am using Clang on Mac. The version information is given as follows.
>>>>
>>>> g++ -v
>>>>
>>>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr
>>>> --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
>>>>
>>>> Apple LLVM version 10.0.0 (clang-1000.10.44.4)
>>>>
>>>> Target: x86_64-apple-darwin18.2.0
>>>>
>>>> Thread model: posix
>>>>
>>>> I notice that "Starting with the 2018_03 release, the RDKit core C++
>>>> code is written in modern C++; for this release that means C++11. "
>>>>
>>>> Actually, I also use -std=c++11 when compiling my C++ source code. I
>>>> also tested RDKit 2018_09_1 and got the similar error. I am wondering how
>>>> to fix this problem.
>>>>
>>>> Thanks.
>>>>
>>>> Yingfeng
>>>>
>>>>
>>>> _______________________________________________
>>>> Rdkit-discuss mailing list
>>>> Rdkit-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>
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